Starting phenix.real_space_refine on Tue Feb 13 19:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/02_2024/6w62_21551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/02_2024/6w62_21551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/02_2024/6w62_21551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/02_2024/6w62_21551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/02_2024/6w62_21551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/02_2024/6w62_21551.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 30 5.16 5 C 4602 2.51 5 N 1293 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6877 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 29, 'TRANS': 880} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 321 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 16} Time building chain proxies: 4.90, per 1000 atoms: 0.66 Number of scatterers: 7387 At special positions: 0 Unit cell: (79.8, 122.85, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 24 15.00 O 1438 8.00 N 1293 7.00 C 4602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 52.7% alpha, 6.7% beta 5 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.503A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 removed outlier: 4.085A pdb=" N TYR A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 308 through 331 removed outlier: 4.363A pdb=" N ILE A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.913A pdb=" N GLU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 423 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.864A pdb=" N ASP A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.651A pdb=" N ARG A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 721 removed outlier: 4.168A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 778 removed outlier: 4.523A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.765A pdb=" N LEU A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 916 through 929 removed outlier: 3.515A pdb=" N VAL A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.534A pdb=" N GLU A 970 " --> pdb=" O THR A 967 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 971 " --> pdb=" O PRO A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 971' Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.699A pdb=" N ARG A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 3.630A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 removed outlier: 3.686A pdb=" N PHE A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.517A pdb=" N ALA A 629 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.819A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.786A pdb=" N GLY A 479 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 486 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 515 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.179A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 642 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.633A pdb=" N TYR A 695 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 963 through 966 removed outlier: 3.949A pdb=" N PHE A1040 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050 removed outlier: 3.962A pdb=" N THR A1059 " --> pdb=" O VAL A1070 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.45: 1159 1.45 - 1.57: 4056 1.57 - 1.69: 47 1.69 - 1.81: 51 Bond restraints: 7573 Sorted by residual: bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N SER A 490 " pdb=" CA SER A 490 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.41e-02 5.03e+03 8.79e+00 bond pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N VAL A 686 " pdb=" CA VAL A 686 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 7.91e+00 bond pdb=" N SER A 803 " pdb=" CA SER A 803 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.51e+00 ... (remaining 7568 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 298 106.89 - 113.67: 4252 113.67 - 120.46: 2925 120.46 - 127.24: 2771 127.24 - 134.03: 100 Bond angle restraints: 10346 Sorted by residual: angle pdb=" N PRO A 491 " pdb=" CA PRO A 491 " pdb=" C PRO A 491 " ideal model delta sigma weight residual 113.53 124.09 -10.56 1.39e+00 5.18e-01 5.77e+01 angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.25 110.62 -7.37 1.05e+00 9.07e-01 4.93e+01 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" CB PRO A 955 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.29e+01 angle pdb=" N PRO A 339 " pdb=" CA PRO A 339 " pdb=" CB PRO A 339 " ideal model delta sigma weight residual 103.23 110.01 -6.78 1.07e+00 8.73e-01 4.02e+01 angle pdb=" C ILE A 488 " pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 120.46 126.77 -6.31 1.37e+00 5.33e-01 2.12e+01 ... (remaining 10341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 4499 35.75 - 71.50: 124 71.50 - 107.25: 15 107.25 - 142.99: 0 142.99 - 178.74: 2 Dihedral angle restraints: 4640 sinusoidal: 1966 harmonic: 2674 Sorted by residual: dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual 232.00 53.26 178.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B -11 " pdb=" C1' C B -11 " pdb=" N1 C B -11 " pdb=" C2 C B -11 " ideal model delta sinusoidal sigma weight residual 232.00 55.42 176.58 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1076 0.069 - 0.137: 96 0.137 - 0.206: 6 0.206 - 0.275: 3 0.275 - 0.343: 2 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA SER A 490 " pdb=" N SER A 490 " pdb=" C SER A 490 " pdb=" CB SER A 490 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA LEU A 799 " pdb=" N LEU A 799 " pdb=" C LEU A 799 " pdb=" CB LEU A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1180 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 798 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER A 798 " -0.060 2.00e-02 2.50e+03 pdb=" O SER A 798 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 799 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 674 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO A 675 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 845 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ALA A 845 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 845 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 846 " 0.013 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 78 2.49 - 3.09: 5914 3.09 - 3.69: 11592 3.69 - 4.30: 16348 4.30 - 4.90: 25760 Nonbonded interactions: 59692 Sorted by model distance: nonbonded pdb=" O2' U B -5 " pdb=" OP1 G B -4 " model vdw 1.883 2.440 nonbonded pdb=" O2' G B 1 " pdb=" O5' C B 2 " model vdw 2.064 2.440 nonbonded pdb=" N VAL A 686 " pdb=" OD1 ASP A 696 " model vdw 2.198 2.520 nonbonded pdb=" O SER A 798 " pdb=" N SER A 800 " model vdw 2.201 2.520 nonbonded pdb=" OH TYR A 473 " pdb=" O LYS A 619 " model vdw 2.204 2.440 ... (remaining 59687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.910 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7573 Z= 0.220 Angle : 0.642 10.557 10346 Z= 0.410 Chirality : 0.043 0.343 1183 Planarity : 0.004 0.074 1236 Dihedral : 16.092 178.742 2906 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.22 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.27), residues: 900 helix: 0.41 (0.25), residues: 439 sheet: -2.39 (0.50), residues: 101 loop : -3.38 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 79 HIS 0.004 0.001 HIS A 459 PHE 0.015 0.001 PHE A 51 TYR 0.012 0.001 TYR A 995 ARG 0.012 0.001 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 821 LEU cc_start: 0.5408 (tp) cc_final: 0.5177 (tp) REVERT: A 880 LEU cc_start: 0.8182 (mm) cc_final: 0.7961 (mm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1906 time to fit residues: 35.8512 Evaluate side-chains 111 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 459 HIS A 477 ASN A 592 GLN A 600 GLN A 771 HIS A 993 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7573 Z= 0.261 Angle : 0.698 8.698 10346 Z= 0.361 Chirality : 0.044 0.175 1183 Planarity : 0.004 0.058 1236 Dihedral : 17.046 179.242 1356 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.00 % Favored : 88.78 % Rotamer: Outliers : 2.38 % Allowed : 10.10 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.27), residues: 900 helix: 0.32 (0.24), residues: 450 sheet: -2.28 (0.56), residues: 80 loop : -3.16 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 79 HIS 0.006 0.001 HIS A 662 PHE 0.030 0.002 PHE A1047 TYR 0.013 0.002 TYR A 996 ARG 0.002 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8164 (mm-40) REVERT: A 77 VAL cc_start: 0.8284 (t) cc_final: 0.8021 (p) REVERT: A 80 PHE cc_start: 0.7978 (m-80) cc_final: 0.7760 (m-80) REVERT: A 674 LEU cc_start: 0.7805 (pp) cc_final: 0.7593 (pp) REVERT: A 758 MET cc_start: 0.7502 (tmm) cc_final: 0.7181 (tmm) REVERT: A 880 LEU cc_start: 0.8208 (mm) cc_final: 0.7955 (mm) REVERT: A 968 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.8178 (Cg_endo) outliers start: 16 outliers final: 14 residues processed: 134 average time/residue: 0.1968 time to fit residues: 35.9449 Evaluate side-chains 120 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 1057 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 477 ASN A 862 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7573 Z= 0.193 Angle : 0.650 9.349 10346 Z= 0.331 Chirality : 0.042 0.171 1183 Planarity : 0.004 0.062 1236 Dihedral : 17.027 179.315 1356 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.57 % Allowed : 14.41 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.28), residues: 900 helix: 0.47 (0.24), residues: 449 sheet: -2.31 (0.56), residues: 81 loop : -3.12 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 79 HIS 0.009 0.001 HIS A 367 PHE 0.020 0.002 PHE A1047 TYR 0.016 0.002 TYR A 116 ARG 0.002 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6578 (tpt) cc_final: 0.6332 (tpt) REVERT: A 50 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8018 (mm-40) REVERT: A 80 PHE cc_start: 0.7827 (m-80) cc_final: 0.7578 (m-80) REVERT: A 758 MET cc_start: 0.7676 (tmm) cc_final: 0.7261 (tmm) REVERT: A 880 LEU cc_start: 0.8122 (mm) cc_final: 0.7868 (mm) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 0.1734 time to fit residues: 32.7902 Evaluate side-chains 120 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7573 Z= 0.345 Angle : 0.748 8.021 10346 Z= 0.390 Chirality : 0.047 0.209 1183 Planarity : 0.005 0.068 1236 Dihedral : 17.169 177.580 1356 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 5.05 % Allowed : 15.01 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.27), residues: 900 helix: 0.02 (0.23), residues: 457 sheet: -2.29 (0.55), residues: 80 loop : -3.20 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 79 HIS 0.012 0.002 HIS A 367 PHE 0.018 0.002 PHE A1047 TYR 0.018 0.002 TYR A 473 ARG 0.004 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7262 (mp) cc_final: 0.6366 (mm) REVERT: A 50 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7797 (mm-40) REVERT: A 77 VAL cc_start: 0.8347 (t) cc_final: 0.7933 (p) REVERT: A 80 PHE cc_start: 0.8095 (m-80) cc_final: 0.7880 (m-80) REVERT: A 650 ILE cc_start: 0.6603 (pt) cc_final: 0.6401 (pt) REVERT: A 758 MET cc_start: 0.8027 (tmm) cc_final: 0.7300 (tmm) REVERT: A 802 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4768 (pp) REVERT: A 880 LEU cc_start: 0.8190 (mm) cc_final: 0.7869 (mm) outliers start: 34 outliers final: 21 residues processed: 133 average time/residue: 0.1532 time to fit residues: 29.8172 Evaluate side-chains 129 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS A 407 GLN A 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7573 Z= 0.188 Angle : 0.656 9.342 10346 Z= 0.333 Chirality : 0.042 0.183 1183 Planarity : 0.004 0.067 1236 Dihedral : 17.074 179.474 1356 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.16 % Allowed : 17.38 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.28), residues: 900 helix: 0.35 (0.24), residues: 457 sheet: -2.17 (0.57), residues: 79 loop : -3.07 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 79 HIS 0.015 0.001 HIS A 367 PHE 0.019 0.002 PHE A 476 TYR 0.011 0.001 TYR A 116 ARG 0.002 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7248 (mp) cc_final: 0.6391 (mm) REVERT: A 50 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7791 (mm-40) REVERT: A 707 TYR cc_start: 0.6533 (t80) cc_final: 0.5990 (t80) REVERT: A 758 MET cc_start: 0.8157 (tmm) cc_final: 0.7457 (tmm) REVERT: A 880 LEU cc_start: 0.8154 (mm) cc_final: 0.7832 (mm) REVERT: A 913 MET cc_start: 0.4049 (mmm) cc_final: 0.3578 (tpp) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.1662 time to fit residues: 31.6084 Evaluate side-chains 125 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7573 Z= 0.201 Angle : 0.673 10.090 10346 Z= 0.339 Chirality : 0.044 0.236 1183 Planarity : 0.004 0.067 1236 Dihedral : 17.048 179.399 1356 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 5.20 % Allowed : 18.13 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.28), residues: 900 helix: 0.44 (0.24), residues: 459 sheet: -2.13 (0.58), residues: 79 loop : -3.11 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 79 HIS 0.003 0.001 HIS A 366 PHE 0.022 0.002 PHE A 476 TYR 0.013 0.001 TYR A 437 ARG 0.003 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7317 (mp) cc_final: 0.6412 (mm) REVERT: A 50 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7821 (mm-40) REVERT: A 78 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7247 (t0) REVERT: A 448 ILE cc_start: 0.3222 (tt) cc_final: 0.2945 (tt) REVERT: A 707 TYR cc_start: 0.6489 (t80) cc_final: 0.5968 (t80) REVERT: A 758 MET cc_start: 0.8112 (tmm) cc_final: 0.7522 (tmm) REVERT: A 802 LEU cc_start: 0.5092 (OUTLIER) cc_final: 0.3916 (tp) REVERT: A 880 LEU cc_start: 0.8104 (mm) cc_final: 0.7759 (mm) outliers start: 35 outliers final: 27 residues processed: 138 average time/residue: 0.1689 time to fit residues: 32.7823 Evaluate side-chains 136 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7573 Z= 0.264 Angle : 0.719 9.956 10346 Z= 0.362 Chirality : 0.046 0.268 1183 Planarity : 0.004 0.074 1236 Dihedral : 17.035 179.211 1356 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 5.35 % Allowed : 19.32 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.28), residues: 900 helix: 0.28 (0.24), residues: 458 sheet: -2.28 (0.56), residues: 84 loop : -3.14 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 79 HIS 0.004 0.001 HIS A 367 PHE 0.014 0.002 PHE A1047 TYR 0.024 0.002 TYR A 995 ARG 0.007 0.001 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7400 (mp) cc_final: 0.6540 (mm) REVERT: A 50 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7746 (mm-40) REVERT: A 758 MET cc_start: 0.8073 (tmm) cc_final: 0.7363 (tmm) REVERT: A 802 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.4784 (tp) REVERT: A 880 LEU cc_start: 0.8137 (mm) cc_final: 0.7802 (mm) outliers start: 36 outliers final: 29 residues processed: 132 average time/residue: 0.1681 time to fit residues: 31.6489 Evaluate side-chains 135 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7573 Z= 0.185 Angle : 0.679 11.838 10346 Z= 0.338 Chirality : 0.043 0.238 1183 Planarity : 0.004 0.074 1236 Dihedral : 16.952 179.044 1356 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 5.20 % Allowed : 19.91 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 900 helix: 0.46 (0.24), residues: 461 sheet: -2.06 (0.56), residues: 85 loop : -3.09 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP A 79 HIS 0.003 0.001 HIS A 366 PHE 0.026 0.002 PHE A 783 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7739 (mm-40) REVERT: A 77 VAL cc_start: 0.8509 (t) cc_final: 0.8103 (p) REVERT: A 650 ILE cc_start: 0.6575 (pt) cc_final: 0.6288 (pt) REVERT: A 758 MET cc_start: 0.8091 (tmm) cc_final: 0.7512 (tmm) REVERT: A 802 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4674 (tp) REVERT: A 880 LEU cc_start: 0.8097 (mm) cc_final: 0.7741 (mm) outliers start: 35 outliers final: 28 residues processed: 144 average time/residue: 0.1740 time to fit residues: 35.2433 Evaluate side-chains 137 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7573 Z= 0.232 Angle : 0.709 11.467 10346 Z= 0.358 Chirality : 0.045 0.225 1183 Planarity : 0.004 0.075 1236 Dihedral : 16.955 179.786 1356 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 4.61 % Allowed : 21.10 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.28), residues: 900 helix: 0.34 (0.24), residues: 461 sheet: -2.20 (0.56), residues: 84 loop : -3.12 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.003 TRP A 79 HIS 0.004 0.001 HIS A 367 PHE 0.029 0.002 PHE A 783 TYR 0.025 0.002 TYR A 700 ARG 0.006 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7774 (mm-40) REVERT: A 77 VAL cc_start: 0.8419 (t) cc_final: 0.7982 (p) REVERT: A 650 ILE cc_start: 0.6639 (pt) cc_final: 0.6401 (pt) REVERT: A 758 MET cc_start: 0.8096 (tmm) cc_final: 0.7512 (tmm) REVERT: A 802 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4171 (tp) REVERT: A 880 LEU cc_start: 0.8151 (mm) cc_final: 0.7813 (mm) outliers start: 31 outliers final: 28 residues processed: 134 average time/residue: 0.1800 time to fit residues: 33.7812 Evaluate side-chains 136 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 0.0270 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7573 Z= 0.165 Angle : 0.686 13.268 10346 Z= 0.344 Chirality : 0.044 0.257 1183 Planarity : 0.004 0.071 1236 Dihedral : 16.871 177.508 1356 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.27 % Allowed : 22.88 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.28), residues: 900 helix: 0.59 (0.24), residues: 455 sheet: -2.12 (0.55), residues: 90 loop : -3.05 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.004 TRP A 79 HIS 0.003 0.001 HIS A 126 PHE 0.024 0.002 PHE A 476 TYR 0.021 0.001 TYR A 995 ARG 0.006 0.001 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 74 LEU cc_start: 0.8018 (tt) cc_final: 0.7726 (tp) REVERT: A 77 VAL cc_start: 0.8450 (t) cc_final: 0.8021 (p) REVERT: A 650 ILE cc_start: 0.6318 (pt) cc_final: 0.6071 (pt) REVERT: A 758 MET cc_start: 0.8066 (tmm) cc_final: 0.7497 (tmm) REVERT: A 785 LEU cc_start: 0.7144 (mm) cc_final: 0.6679 (mm) REVERT: A 802 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.4832 (tp) REVERT: A 880 LEU cc_start: 0.8136 (mm) cc_final: 0.7855 (mm) outliers start: 22 outliers final: 19 residues processed: 132 average time/residue: 0.1678 time to fit residues: 31.6000 Evaluate side-chains 127 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.162327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.143213 restraints weight = 15656.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.146837 restraints weight = 9254.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.149139 restraints weight = 6309.204| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 7573 Z= 0.290 Angle : 1.040 59.196 10346 Z= 0.613 Chirality : 0.050 0.622 1183 Planarity : 0.005 0.075 1236 Dihedral : 16.881 177.508 1356 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.44 % Favored : 90.44 % Rotamer: Outliers : 3.57 % Allowed : 23.18 % Favored : 73.25 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.28), residues: 900 helix: 0.59 (0.24), residues: 455 sheet: -2.05 (0.56), residues: 90 loop : -3.04 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.005 TRP A 79 HIS 0.003 0.001 HIS A 366 PHE 0.022 0.002 PHE A 718 TYR 0.020 0.002 TYR A 995 ARG 0.005 0.000 ARG A 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.30 seconds wall clock time: 30 minutes 59.22 seconds (1859.22 seconds total)